Application of DArT seq derived SNP tags for comparative genome analysis in fishes; An alternative pipeline using sequence data from a non-traditional model species, Macquaria ambigua

Autoři: Foyez Shams aff001;  Fiona Dyer aff001;  Ross Thompson aff001;  Richard P. Duncan aff001;  Jason D. Thiem aff003;  Andrzej Kilian aff001;  Tariq Ezaz aff001
Působiště autorů: Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia aff001;  Centre for Applied Water Science, University of Canberra, Canberra, Australian Capital Territory, Australia aff002;  Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, New South Wales, Australia aff003;  Diversity Arrays Technology, Bruce, Australian Capital Territory, Australia aff004
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
doi: 10.1371/journal.pone.0226365


Bi-allelic Single Nucleotide Polymorphism (SNP) markers are widely used in population genetic studies. In most studies, sequences either side of the SNPs remain unused, although these sequences contain information beyond that used in population genetic studies. In this study, we show how these sequence tags either side of a single nucleotide polymorphism can be used for comparative genome analysis. We used DArTseq (Diversity Array Technology) derived SNP data for a non-model Australian native freshwater fish, Macquaria ambigua, to identify genes linked to SNP associated sequence tags, and to discover homologies with evolutionarily conserved genes and genomic regions. We concatenated 6,776 SNP sequence tags to create a hypothetical genome (representing 0.1–0.3% of the actual genome), which we used to find sequence homologies with 12 model fish species using the Ensembl genome browser with stringent filtering parameters. We identified sequence homologies for 17 evolutionarily conserved genes (cd9b, plk2b, rhot1b, sh3pxd2aa, si:ch211-148f13.1, si:dkey-166d12.2, zgc:66447, atp8a2, clvs2, lyst, mkln1, mnd1, piga, pik3ca, plagl2, rnf6, sec63) along with an ancestral evolutionarily conserved syntenic block (euteleostomi Block_210). Our analysis also revealed repetitive sequences covering approximately 12% of the hypothetical genome where DNA transposon, LTR and non-LTR retrotransposons were most abundant. A hierarchical pattern of the number of sequence homologies with phylogenetically close species validated the approach for repeatability. This new approach of using SNP associated sequence tags for comparative genome analysis may provide insight into the genome evolution of non-model species where whole genome sequences are unavailable.

Klíčová slova:

Comparative genomics – DNA sequence analysis – Evolutionary genetics – Genome analysis – Genome evolution – Multiple alignment calculation – Sequence alignment – Sticklebacks


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2019 Číslo 12